rs7550106

chr1-152224726-T-Cchr1-152224726-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653548.1(FLG-AS1):n.166-24169T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,080 control chromosomes in the GnomAD database, including 37,181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (37181 hom., cov: 32)
• Consequence: FLG-AS1 ENST00000653548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

FLG-AS1 (HGNC:27913): (cervical cancer associated DHX9 suppressive transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLG-AS1	ENST00000653548.1	n.166-24169T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102492 AN: 151962 Hom.: 37159 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.681

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.674 AC: 102541 AN: 152080 Hom.: 37181 Cov.: 32 AF XY: 0.667 AC XY: 49604 AN XY: 74344

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.685

Alfa AF: 0.741 Hom.: 7392

Bravo AF: 0.649

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.7
Dann	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7550106; hg19: chr1-152197202;